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7 """Bio.SeqIO support for the "genbank" and "embl" file formats.
8
9 You are expected to use this module via the Bio.SeqIO functions.
10 Note that internally this module calls Bio.GenBank to do the actual
11 parsing of both GenBank and EMBL files.
12
13 See also:
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15 International Nucleotide Sequence Database Collaboration
16 http://www.insdc.org/
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18 GenBank
19 http://www.ncbi.nlm.nih.gov/Genbank/
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21 EMBL Nucleotide Sequence Database
22 http://www.ebi.ac.uk/embl/
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24 DDBJ (DNA Data Bank of Japan)
25 http://www.ddbj.nig.ac.jp/
26 """
27
28 from Bio.GenBank.Scanner import GenBankScanner, EmblScanner
29 from Bio.Alphabet import generic_protein
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38 """Breaks up a Genbank file into SeqRecord objects.
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40 Every section from the LOCUS line to the terminating // becomes
41 a single SeqRecord with associated annotation and features.
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43 Note that for genomes or chromosomes, there is typically only
44 one record."""
45
46 return GenBankScanner(debug=0).parse_records(handle)
47
49 """Breaks up an EMBL file into SeqRecord objects.
50
51 Every section from the LOCUS line to the terminating // becomes
52 a single SeqRecord with associated annotation and features.
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54 Note that for genomes or chromosomes, there is typically only
55 one record."""
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57 return EmblScanner(debug=0).parse_records(handle)
58
60 """Breaks up a Genbank file into SeqRecord objects for each CDS feature.
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62 Every section from the LOCUS line to the terminating // can contain
63 many CDS features. These are returned as with the stated amino acid
64 translation sequence (if given).
65 """
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67 return GenBankScanner(debug=0).parse_cds_features(handle, alphabet)
68
70 """Breaks up a EMBL file into SeqRecord objects for each CDS feature.
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72 Every section from the LOCUS line to the terminating // can contain
73 many CDS features. These are returned as with the stated amino acid
74 translation sequence (if given).
75 """
76
77 return EmblScanner(debug=0).parse_cds_features(handle, alphabet)
78